Wind Waker Ganondorf. It's probably because of him that I love the game so much.
Twilight Princess Ganondorf was evil, yes, and he had some very taunting lines, such as the one Shrukan mentioned... However, the Wind Waker Ganondorf, in my opinion, had more emotion to him. He was given more characterization, and when he was killed off, you would actually feel bad for him. He was crazy in a sense, yet he kept to his own personal goal... When it was crushed, that is when you realize just how mortal he is, no different than you and me.
That's just how I view it.